Microbial residues are important sources for stabilizing soil carbon pools and are of great significance for carbon sequestration and accumulation in the degraded habitats. Plant root exudates, as the medium of plant-soil-microorganism linkages, play a key role in regulating the migration and transformation of soil microbial residues. In this study, we simulated the effects of different nitrogen concentrations (low nitrogen-LN:0.1 gN/kg; high nitrogen-HN:0.2 gN/kg) and diversities (3 compounds, 9 compounds) of root exudates on soil microbial residues in extremely degraded grassland soils with amino sugars as markers. The results showed that:(1) the input of root exudates significantly increased the content of soil microbial residues in alpine degraded grassland, which was mainly contributed by fungal residues. The microbial and fungal residues increased by 101.14% and 125.16% in the high nitrogen and low diversity treatments, respectively, while only increased by 35.79% and 33.51% in the low nitrogen and high diversity treatments. (2) The input of root exudates increased the activities of β-glucosidase, acid phosphatase and peroxidase in soil and promoted the growth of microorganisms, while decreased the activities of β-N-acetaminoglycosidase and reduced the decomposition of microbial residues. (3) Regression analysis showed that soil microbial residues were significantly negatively correlated with soil environment C/N, and significantly positively correlated with microbial biomass C/N. The results showed that the soil carbon sequestration strategy simulating the input of root exudates could be fully utilized in the future restoration of degraded grassland, which could promote microbial growth, accelerate metabolic turnover and further increase microbial residues content by improving the availability of soil nitrogen.